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From: Baker, N. <nat...@pn...> - 2020-09-25 02:02:45
|
Hi All – This mailing list is shutting down and moving to MailChimp. Please subscribe to the MailChimp list at https://poissonboltzmann.us11.list-manage.com/subscribe?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0 Thank you, -- Nathan Baker http://pronoun.is/he Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab Department of Applied Mathematics — University of Washington https://www.linkedin.com/in/nathanandrewbaker/ |
From: Jurrus, E. R <Eli...@pn...> - 2016-03-26 13:51:06
|
Dear APBS and PDB2PQR users – We are pleased to announce the release of PDB2PQR 2.1 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade. Please see http://www.poissonboltzmann.org/news/comp_pdb2pqr_release_history/ for the complete release notes. Thank you for your continued support of APBS and PDB2PQR. Sincerely, The APBS/PDB2PQR development team Notable new features: The old Monte Carlo method has been replaced with graph cut. See http://arxiv.org/abs/1507.07021 (To use the original Monte Carlo method, see verion 2.0) NEW FEATURES * Added alternate method to do visualization using 3dmol. * Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/) * Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly. * Added a check before calculating pKa's for large interactions energies. BUG FIXES * Fixed broken links on APBS submission page. * Added some missing files to querystaus page results. * Fixed some pages to use the proper CSS file. * Better error message for --assign-only and HIS residues. * Fix PROPKA crash for unrecognized residue. * Debumping routines are now more consistent across platforms. This fixes pdb2pka not giving the same results on different platforms. CHANGES * Added fabric script used to build and test releases. * The networkx library is now required for pdb2pka. KNOWN BUGS * If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter. * Running ligands and PDB2PKA at the same time is not currently supported. * PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (ie ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM ( 60 titratable residues will use 480MB ). We are working to fix this. |
From: Nathan B. <nat...@gm...> - 2016-01-09 03:44:18
|
Dear APBS & PDB2PQR users -- You are receiving this message because you are still subscribed to the old APBS/PDB2PQR mailing lists. Please update your subscription to the new lists by visiting http://eepurl.com/by4eQr. Thank you for your continued support of APBS and PDB2PQR! Sincerely, The APBS & PDB2PQR Development Team ---------- Forwarded message --------- From: APBS & PDB2PQR Biomolecular Solvation Software < nat...@gm...> Date: Fri, Jan 8, 2016 at 7:41 PM Subject: APBS 1.4.2 now available To: Nathan <nat...@ic...> APBS 1.4.2 is now available View this email in your browser <http://us11.campaign-archive1.com/?u=a5808042b2b3ea90ee3603cd8&id=f32947e2b6&e=cbebd7d419> APBS 1.4.2 is now available ------------------------------ Dear APBS and PDB2PQR users: We are pleased to announce the release of APBS 1.4.2 which is now available on GitHub <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=9a1baad17f&e=cbebd7d419> and SourceForge <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=77d115c85f&e=cbebd7d419>. New features and bug fixes for this release are described below. The latest information about APBS and PDB2PQR can always be found at http://www.poissonboltzmann.org/ <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=ed8a78d648&e=cbebd7d419> . Thank you for your continued support of APBS! Sincerely, The APBS & PDB2PQR Development Team ------------------------------ New Features - Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and built with APBS - New Geometric flow API and improvements in speed (#235 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b6e24daad1&e=cbebd7d419> ) - Support for BinaryDX file format (#216 <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=173ddd0bde&e=cbebd7d419> ) - SOR solver added for mg-auto input file option - DXMath improvements (#168 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=53e3362d88&e=cbebd7d419> , #216 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=012e20cdf4&e=cbebd7d419> ) - Test suite improvements - APBS build in Travis-CI - Geometric Flow tests added - Protein RNA tests enabled (#149 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=5d69d102ef&e=cbebd7d419> ) - Intermetiate result testing (#64 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=709a649568&e=cbebd7d419> ) - Example READMEs onverted to markdown and updated with latest results Bug Fixes - OpenMPI (mg-para) functionality restored (#190 <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=f6cfc353ba&e=cbebd7d419> ) - Fixed parsing PQR files that contained records other than *ATOM* and *HETATM* (#77 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=0c07b2c433&e=cbebd7d419> , #214 <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=c3b3b00013&e=cbebd7d419> ) - Geometric Flow boundary indexing bug fixed - Build fixes: - Out of source CMake builds are again working - Python library may be built (#372 <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=6c35d8d775&e=cbebd7d419> ) - CentOS 5 binary builds for glibc compatibility - Pull requests merged - Removed irrelevant warning messages (#378 <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=eefca7cc05&e=cbebd7d419> ) Notes The following packages are treated as submodules in APBS: - Geometric Flow has been moved to its own repository <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b7e0599ca8&e=cbebd7d419> - FETk has been cloned <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=13baff3b2b&e=cbebd7d419> so that we have could effect updates - PB-SAM lives here <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=bd09191b31&e=cbebd7d419> We have added a chat feature <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=31e3a5c86a&e=cbebd7d419> for users. This can also be found from the support tab on http://www.poissonboltzmann.org/ <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=68bc8771d1&e=cbebd7d419> . Known Bugs - Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that doth not support C++11. This is also an issue for CentOS 5 - BEM is temprarily disabled due to build issues - Geometric Flow build is currently broken on Windows using Visual Studio <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=fac3dbf2ae&e=cbebd7d419> *Copyright © 2016 APBS & PDB2PQR Biomolecular Solvation Software, All rights reserved.* You are receiving this email because you opted in when registering your use of the APBS/PDB2PQR software. *Our mailing address is:* APBS & PDB2PQR Biomolecular Solvation Software PO Box 999, MSID K7-20 c/o Nathan Baker Richland, WA 99352 Add us to your address book <http://poissonboltzmann.us11.list-manage.com/vcard?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0> Want to change how you receive these emails? You can update your preferences <http://poissonboltzmann.us11.list-manage1.com/profile?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=cbebd7d419> or unsubscribe from this list <http://poissonboltzmann.us11.list-manage.com/unsubscribe?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=cbebd7d419&c=f32947e2b6> |
From: Nathan B. <nat...@gm...> - 2015-10-08 18:04:11
|
Dear APBS & PDB2PQR users -- I apologize for the additional email but we are having difficulties porting our mailing lists to MailChimp due to its safeguards against spam and unsolicited subscriptions. Therefore, we'd like your help in signing up for this new list by filling out the form at *http://eepurl.com/by4eQr <http://eepurl.com/by4eQr>* Thank you for your help and please accept our apologies for the additional step. Sincerely, The APBS & PDB2PQR Development Team On Wed, Sep 16, 2015 at 6:42 AM, APBS & PDB2PQR Biomolecular Solvation Software <nat...@gm...> wrote: > Moving the APBS/PDB2PQR mailing lists to MailChimp! View this email in > your browser > <http://us11.campaign-archive2.com/?u=a5808042b2b3ea90ee3603cd8&id=d2fe1643e9&e=5eda05f532> Dear > APBS & PDB2PQR users -- > > Over the past few months, we have been migrating APBS/PDB2PQR resources > from SourceForge to other sites such as GitHub ( > https://github.com/Electrostatics > <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=4adba9ada4&e=5eda05f532>). > In the next few days, we will be moving the APBS and PDB2PQR announcements > mailing lists to MailChimp (http://www.mailchimp.com > <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=985ae31007&e=5eda05f532>). > Once this migration is complete, we will be sending a message from the new > mailing list requesting your feedback on possible replacements for the APBS > and PDB2PQR user mailing lists (e.g., StackExchange, Slack, Google Groups, > LinkedIn, etc.). > > No action is required on your part. However, if you are curious about the > new mailing list, we'd appreciate your help testing our new APBS/PDB2PQR > registration form at http://eepurl.com/by4eQr > <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=ef843c133d&e=5eda05f532> > . > > Thank you for your continuing support of APBS and PDB2PQR. > > Sincerely, > > The APBS & PDB2PQR Development Team > <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=9f6e7949f7&e=5eda05f532> > <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=f6d5ecb2bb&e=5eda05f532> > <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=18c8dcbdc9&e=5eda05f532> *Copyright > © 2015 APBS & PDB2PQR Biomolecular Solvation Software, All rights reserved.* > You are receiving this email because you opted in when registering your > use of the APBS/PDB2PQR software. > > *Our mailing address is:* > APBS & PDB2PQR Biomolecular Solvation Software > PO Box 999, MSID K7-20 > c/o Nathan Baker > Richland, WA 99352 > > Add us to your address book > <http://poissonboltzmann.us11.list-manage.com/vcard?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0> > > > Want to change how you receive these emails? > You can update your preferences > <http://poissonboltzmann.us11.list-manage.com/profile?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=5eda05f532> > or unsubscribe from this list > <http://poissonboltzmann.us11.list-manage1.com/unsubscribe?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0&e=5eda05f532&c=d2fe1643e9> > > [image: Email Marketing Powered by MailChimp] > <http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm_medium=email&utm_campaign=monkey_rewards&aid=a5808042b2b3ea90ee3603cd8&afl=1> > |
From: Baker, N. <Nat...@pn...> - 2015-09-16 13:34:33
|
Dear APBS & PDB2PQR users -- Over the past few months, we have been migrating APBS/PDB2PQR resources from SourceForge to other sites such as GitHub (https://github.com/Electrostatics). In the next few days, we will be moving the APBS and PDB2PQR announcements mailing lists to MailChimp (http://www.mailchimp.com). Once this migration is complete, we will be sending a message from the new mailing list requesting your feedback on possible replacements for the APBS and PDB2PQR user mailing lists (e.g., StackExchange, Slack, Google Groups, LinkedIn, etc.). No action is required on your part. However, if you are curious about the new mailing list, we'd appreciate your help testing our new APBS/PDB2PQR registration form at http://eepurl.com/by4eQr. Thank you for your continuing support of APBS and PDB2PQR. Sincerely, -- Nathan Baker Laboratory Fellow Computational and Statistical Analytics Division Pacific Northwest National Laboratory +1-509-375-3997 https://goo.gl/H3X8f1 |
From: Baker, N. <Nat...@pn...> - 2014-12-28 11:28:41
|
Dear APBS and PDB2PQR users - We are pleased to announce the release of PDB2PQR 2.0 which is now available from http://www.poissonboltzmann.org/docs/downloads/. There are several improvements and fixes (outlined below) to this release of the software and we encourage all users to upgrade. Please see http://www.poissonboltzmann.org/pdb2pqr/release-history for the complete release notes. Thank you for your continued support of APBS and PDB2PQR. Sincerely, The APBS/PDB2PQR development team Notable new features: PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES * Improved look of web interface * Option to automatically drop water from pdb file before processing. * Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA. * Support for compiling with VS2008 in Windows. * Option to build with debug headers. * PDB2PKA now detects and reports non Henderson-Hasselbalch behavior. * PDB2PKA can be instructed whether or not to start from scratch with --pdb2pka-resume * Can now specify output directory for PDB2PKA. * Improved error regarding backbone in some cases. * Changed time format on querystatus page * Improved error catching on web interface. BUG FIXES * Fixed executable name when creating binaries for Unix based operating systems. * Fixed potential crash when using --clean with extensions. * Fixed MAXATOMS display on server home page. * PDB2PKA now mostly respects the --verbose setting. * Fixed how hydrogens are added by PDB2PKA for state changes in some cases. * Fixed psize error check. * Will now build properly without ligand support if numpy is not installed. * Removed old automake build files from all tests ported to scons. * Fixed broken opal backend. CHANGES * Command line interface to PROPKA changed to accommodate PDB2PKA. PROPKA is now used with --ph-calc-method=propka. --with-ph now defaults to 7.0 and is only required if a different pH value is required. * --ph-calc-method to select optional method to calculate pH values used to protonate titratable residues. Possible options are "propka" and "pdb2pka". * Dropped support for compilation with mingw. Building on Windows now requires VS 2008 installed in the default location. * Updated included Scons to 2.3.3 * PDB2PKA can now be run directly (not integrated in PDB2PQR) with pka.py. Arguments are and . * No longer providing 32-bit binary builds. PDB2PKA support is too memory intensive to make this practical in many cases. KNOWN BUGS * If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter. * Running ligands and PDB2PKA at the same time is not currently supported. * PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (ie ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM ( 60 titratable residues will use 480MB ). We are working to fix this. |
From: Baker, N. <Nat...@pn...> - 2014-08-15 02:41:03
|
Dear APBS users -- We are pleased to announce the release of APBS 1.4.1. This was primarily a bug fix release, however, we have added a few new features we'd like to highlight: * Multigrid bug fix for volumes with large problem domains * We have added a preliminary implementation of geometric flow * Finite element method support has been re-enabled * Migration of the APBS source tree to GitHub (https://github.com/Electrostatics/apbs-pdb2pqr) for better collaboration, issue tracking, and source code management * Improved test suite The new version of APBS can be downloaded from http://www.poissonboltzmann.org/docs/downloads/#downloads. We would also like to highlight our new web site, still located at: http://www.poissonboltzmann.org/. This site is also hosted at GitHub and we hope that the new organization will make it easier for people to find the content they need. While we are still in the process of migrating some remaining content, we have added links to the previous web page when needed. Thank you for your continuing support of APBS. As always, please use our mailing lists to send us questions or comments about our software. Sincerely, The APBS Development Team -- Nathan Baker Laboratory Fellow and Technical Group Manager Applied Statistics and Computational Modeling Group Pacific Northwest National Laboratory +1-509-375-3997 http://www.linkedin.com/in/nathanandrewbaker |
From: Baker, N. <Nat...@pn...> - 2012-10-03 15:34:22
|
Hi Eliana – That’s odd. Can you send the offending PDB file? Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> From: Eliana Asciutto [mailto:eka...@gm...] Sent: Tuesday, October 02, 2012 6:59 AM To: apb...@go... Subject: [apbs-users] capped peptide Hi all, When trying to generate pqr for a capped peptide with charmm or amber force field through the server, the code doesn't recognize the atoms in the term residues and deletes them. Checking for missing heavy atoms... Missing OXT in ALA A 7 Extra atom NT in ALA A 7! - Deleted this atom. Extra atom HNT in ALA A 7! - Deleted this atom. Extra atom CAT in ALA A 7! - Deleted this atom. Extra atom HT1 in ALA A 7! - Deleted this atom. Extra atom HT2 in ALA A 7! - Deleted this atom. Extra atom HT3 in ALA A 7! - Deleted this atom. Since I have also ions in the pdb I need to use charmm or amber in order to have the ions read properly. Any suggestion? Thanks! Eliana . |
From: Baker, N. <Nat...@pn...> - 2012-08-01 18:33:18
|
Dear APBS users -- We are pleased to announce the release of APBS 1.4.0. This version of APBS includes a massive rewrite to eliminate FORTRAN from the software code base to improve portability and facilitate planned optimization and parallelization activities. A more detailed list of changes is provided below. Starting with this release, we have created separate installation packages for the APBS binaries, examples, and programmer's documentation. This change is in response to user requests and recognition of the large size of the examples and documentation directories. As usual, APBS can be freely downloaded from http://www.poissonboltzmann.org/apbs/downloads. Thank you for your continued support of APBS. Sincerely, The APBS Development Team Please see http://www.poissonboltzmann.org/apbs/release-history for the complete change log · Removed FORTRAN dependency from APBS o Direct line by line translation of all source from contrib/pmgZ o Functions replaced and tested incrementally to ensure code congruence o Created new subfolder src/pmgC for translated pmg library o Created new macros for 2d, 3d matrix access § In src/generic/apbs/vmatrix.h § Simulate native FORTRAN 2 and 3 dimensional arrays § Use 1-indexed, column-major ordering § Allowed direct 1-1 translation from FORTRAN to ensurre code congruence · Added additional debugging and output macros to src/generic/apbs/vhal.h o Added message, error message, assertion, warning, and abort macros o Macro behavior modified by the --enable-debug flag for configure § Non-error messages directed to stderr in debug, io.mc otherwise § All error messages are directed to stdout § In debug mode, verbose location information is provided · Added additional flags to configure o --with-fetk replaces FETK_INCLUDE, FETK_LIBRARY environment flags o --with-efence enables compiling with electric fence library o --enable-debug eliminates compiling optimization and includes line no info o --enable-profiling adds profiling information and sets --enable-debug o --enable-verbose-debug prints lots of function specific information |
From: Baker, N. <Nat...@pn...> - 2012-05-22 13:12:10
|
Dear APBS community - I am in the process of writing a renewal proposal for the grant that supports APBS and PDB2PQR development. The impact of these software packages on the user community is an important evaluation criterion for such funding. Therefore, I would very much appreciate if you would be willing to provide examples of how APBS and/or PDB2PQR have played major roles in your research or teaching. Examples that emphasize the critical or unique roles of these packages are particularly important. Any feedback you can provide by Jun 10 would be much appreciated. Thank you for your help and your continued support of APBS and PDB2PQR! __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> |
From: Baker, N. <Nat...@pn...> - 2012-01-11 17:22:33
|
Dear APBS & PDB2PQR Users - It has come to my attention that some of your e-mails have not reached me due to firewall configuration issues. Please address future inquiries to my Gmail address (nat...@gm...<mailto:nat...@gm...>) and/or the APBS/PDB2PQR user mailing lists. Thank you, Nathan Baker __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://nabaker.me |
From: Baker, N. <Nat...@pn...> - 2012-01-04 16:22:05
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Dear APBS users -- We have released a new version of the APBS Windows Installer with the following features: * Ability to customize install path with correct behavior * Interactive command line interface when double-clicking APBS program Please let us know if you have any questions or concerns about this new installer. Thank you for your support of APBS. Sincerely, __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... http://nabaker.me |
From: Baker, N. <Nat...@pn...> - 2011-09-21 14:53:29
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Dear APBS users -- My apologies for the repeated posts on this subject but I wanted to update you on our troubled transition of the mailing lists to Google Groups. Unfortunately, it appears that many users have restricted access to Google Groups because of firewalls set by their countries and/or organizations. Therefore, we will continue to host and archive the lists at two sites: * APBS-USERS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-users or https://groups.google.com/forum/#!forum/apbs-users * APBS-ANNOUNCEMENTS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-announce or https://groups.google.com/forum/#!forum/apbs-announcements Messages posted to one list will be cross-posted to the other list. Archives will also be available for both lists; however, the Google Groups site offers easier searching and browsing mechanisms. Thank you for your patience. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm |
From: Baker, N. <Nat...@pn...> - 2011-09-10 19:52:01
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Hi All -- I'm very sorry but there was a typo in the first URL I sent. The correct address for the mailing list is https://groups.google.com/forum/#!forum/apbs-announcements Thank you for helping us out by subscribing yourself to this new list. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm -----Original Message----- From: Baker, Nathan Sent: Saturday, September 10, 2011 11:20 AM To: 'APBS-ANNOUNCE list (apb...@li...)' Subject: Please help us by subscribing yourself to the new APBS-ANNOUNCE Google Group Hi All -- I apologize for a second posting on this topic but we've encountered a problem with Google Groups limiting the number of invitations we can send. Therefore, I would like request your help in migrating the list: Could you please visit https://groups.google.com/forum/#!forum/apbs-anouncements and subscribe yourself to the new mailing list? Thank you very much for your help! __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm -----Original Message----- From: Baker, Nathan Sent: Thursday, September 08, 2011 7:23 PM To: APBS-ANNOUNCE list (apb...@li...) Subject: [Apbs-announce] APBS-ANNOUNCE mailing list is moving to Google Groups Dear APBS-ANNOUNCE Subscribers -- The APBS-ANNOUNCE mailing list is moving to a new location at Google Groups: https://groups.google.com/forum/#!forum/apbs-announcements This move is based on your requests for APBS mailing lists that are easier to access and search. Over the next few days, you will be receiving an invitation notice to subscribe to the mailing list at its new location. Please accept this invitation so you will receive posts from the new list. Thank you for your continuing support of APBS. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm ------------------------------------------------------------------------------ Why Cloud-Based Security and Archiving Make Sense Osterman Research conducted this study that outlines how and why cloud computing security and archiving is rapidly being adopted across the IT space for its ease of implementation, lower cost, and increased reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ _______________________________________________ apbs-announce mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-announce |
From: Baker, N. <Nat...@pn...> - 2011-09-10 18:22:09
|
Hi All -- I apologize for a second posting on this topic but we've encountered a problem with Google Groups limiting the number of invitations we can send. Therefore, I would like request your help in migrating the list: Could you please visit https://groups.google.com/forum/#!forum/apbs-anouncements and subscribe yourself to the new mailing list? Thank you very much for your help! __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm -----Original Message----- From: Baker, Nathan Sent: Thursday, September 08, 2011 7:23 PM To: APBS-ANNOUNCE list (apb...@li...) Subject: [Apbs-announce] APBS-ANNOUNCE mailing list is moving to Google Groups Dear APBS-ANNOUNCE Subscribers -- The APBS-ANNOUNCE mailing list is moving to a new location at Google Groups: https://groups.google.com/forum/#!forum/apbs-announcements This move is based on your requests for APBS mailing lists that are easier to access and search. Over the next few days, you will be receiving an invitation notice to subscribe to the mailing list at its new location. Please accept this invitation so you will receive posts from the new list. Thank you for your continuing support of APBS. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm ------------------------------------------------------------------------------ Why Cloud-Based Security and Archiving Make Sense Osterman Research conducted this study that outlines how and why cloud computing security and archiving is rapidly being adopted across the IT space for its ease of implementation, lower cost, and increased reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ _______________________________________________ apbs-announce mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-announce |
From: Baker, N. <Nat...@pn...> - 2011-09-09 02:22:43
|
Dear APBS-ANNOUNCE Subscribers -- The APBS-ANNOUNCE mailing list is moving to a new location at Google Groups: https://groups.google.com/forum/#!forum/apbs-announcements This move is based on your requests for APBS mailing lists that are easier to access and search. Over the next few days, you will be receiving an invitation notice to subscribe to the mailing list at its new location. Please accept this invitation so you will receive posts from the new list. Thank you for your continuing support of APBS. Sincerely, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm |
From: Baker, N. <Nat...@pn...> - 2011-04-03 00:06:55
|
Dear APBS and PDB2PQR users -- This is a last reminder about the APBS/PDB2PQR survey which can be accessed at http://tinyurl.com/apbs-survey. Please be sure to respond before the survey closes on May 1 and enter for a chance to win a $25 Amazon.com gift certificate! Thank you for your support, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://signatures.pnl.gov > -----Original Message----- > From: Baker, Nathan > Sent: Wednesday, March 02, 2011 2:20 PM > To: Baker, Nathan > Subject: New APBS & PDB2PQR survey available > > Dear APBS and PDB2PQR users - > > Thank you very much for your continuing interest in and support of > APBS/PDB2PQR. As you know, we take user feedback very seriously and have > created an annual user survey to receive more widespread input into the > project. > > The survey can be accessed at: > > http://tinyurl.com/apbs-survey > > Please take a few minutes to complete this survey; 5 randomly-selected > participants will be awarded $25 Amazon.com gift certificates. This > survey will close on May 1. > > Thank you for your help! > > Sincerely, > > Nathan Baker > > __________________________________________________ > Nathan Baker > Chief Scientist for Signature Science > Pacific Northwest National Laboratory > 902 Battelle Boulevard > P.O. Box 999, MSIN K7-28 > Richland, WA 99352 USA > Tel: 509-375-3997 > nat...@pn... > http://signatures.pnl.gov |
From: Baker, N. <Nat...@pn...> - 2011-03-02 22:20:14
|
Dear APBS and PDB2PQR users - Thank you very much for your continuing interest in and support of APBS/PDB2PQR. As you know, we take user feedback very seriously and have created an annual user survey to receive more widespread input into the project. The survey can be accessed at: http://tinyurl.com/apbs-survey Please take a few minutes to complete this survey; 5 randomly-selected participants will be awarded $25 Amazon.com gift certificates. This survey will close on May 1. Thank you for your help! Sincerely, Nathan Baker __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... http://signatures.pnl.gov |
From: Robert K. <ro...@uc...> - 2011-01-31 23:11:12
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+--------------------------------------------------------------------+ | | | APBS Roll 5.4 Release Announcement | | | +--------------------------------------------------------------------+ The National Biomedical Computation Resource at University of California, San Diego is pleased to announce the availability of APBS Roll package for Rocks clusters version 5.4. APBS (Adaptive Poisson-Boltzmann Solver) is a scalable Poisson-Boltzmann equation solver used to study electrostatic properties of small to nanoscale biomolecular systems. The APBS Roll simplifies APBS deployment and integration on Rocks clusters (http://www.rocksclusters.org). More information about APBS can be found at http://apbs.sourceforge.net/ or at http://www.nbcr.net. This APBS Roll contains the latest APBS version 1.3 and PDB2PQR package version 1.7. The APBS Roll can be downloaded from the APBS download site http://www.poissonboltzmann.org/apbs and the Roll documentation including installation and usage information is available at http://nbcr.net/software/doc/apbs-roll/5.4/ Questions or comments about the roll may be directed to Robert Konecny <ro...@uc...>. |
From: Baker, N. <Nat...@pn...> - 2010-10-27 14:54:51
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Dear APBS users -- We are pleased to announce the release of APBS 1.3. This release contains several new features and bug fixes which are described in detail at http://goo.gl/l0Pt. Among these changes are several important features which should be of broad interest to the community. * The primary URL for APBS Opal support has changed to leverage services provided by the National Biomedical Computation Resource (http://nbcr.net/). This provides additional computational resources to users who are interested in running calculations on remote resources, as described at http://goo.gl/CHZy. * APBS now supports the ability to write out atom-specific potentials using the "write atompot" keyword in the APBS input file. This has been an often-requested feature and is described in more detail at http://goo.gl/iEAO. * APBS now supports the ability to read and write compressed (GZIPped) potential file output using the "write pot gz ..." command (see http://goo.gl/iEAO). * APBS now provides additional control over the numerical accuracy of the underlying calculations, giving users the opportunity to increase/decrease accuracy to change the speed of their calculations. The new version of APBS can be downloaded from http://www.poissonboltzmann.org/apbs/downloads. Thank you for your continuing support of APBS. Sincerely, The APBS Development Team __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... www.pnl.gov |
From: Baker, N. <Nat...@pn...> - 2010-10-13 16:38:25
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Dear APBS and PDB2PQR users -- I am happy to announce the release of PDB2PQR 1.7 which includes two major updates: * For PDB2PQR web interface users: the JMol web interface for APBS calculation visualization has been substantially improved, thanks to help from Bob Hanson. Those performing APBS calculations via the PDB2PQR web interface now have a much wider range of options for visualizing the output online -- as well as downloading for offline analysis. * For PDB2PQR command-line and custom web interface users: the Opal service URLs have changed to new NBCR addresses. Old services hosted at *.wustl.edu addresses have been decommissioned. Please upgrade ASAP to use the new web service. Thank you as always to the staff at NBCR for their continuing support of APBS/PDB2PQR web servers and services. You can learn more about the latest version of PDB2PQR at http://www.poissonboltzmann.org/pdb2pqr. Access to the web interface and to downloads can be found at http://www.poissonboltzmann.org/pdb2pqr/d. Thank you for your continuing support of PDB2PQR. Sincerely, The PDB2PQR Development Team __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... www.pnl.gov |
From: Baker, N. <Nat...@pn...> - 2010-07-23 16:21:42
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Hi All -- I am writing to make you aware of a new software package, APBSmem, developed by Michael Grabe and Keith Callenberg. APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. Many of you have tried the APBS membrane electrostatics tutorial developed by the Grabe lab (http://is.gd/dDq2i); APBSmem facilitates the setup and execution of those types of calculations. Please visit the APBSmem webpage to learn more about this new resource: http://sourceforge.net/projects/apbsmem/ Sincerely, Nathan Baker __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-28 Richland, WA 99352 USA Tel: 509-375-3997 nat...@pn... www.pnl.gov |
From: Robert K. <ro...@uc...> - 2010-02-04 18:42:50
|
+--------------------------------------------------------------------+ | | | APBS Roll 5.3 Release Announcement | | | +--------------------------------------------------------------------+ The National Biomedical Computation Resource at University of California, San Diego is pleased to announce the availability of APBS Roll package for Rocks clusters version 5.3. APBS (Adaptive Poisson-Boltzmann Solver) is a scalable Poisson-Boltzmann equation solver used to study electrostatic properties of small to nanoscale biomolecular systems. The APBS Roll simplifies APBS deployment and integration on Rocks clusters (http://www.rocksclusters.org). More information about APBS can be found at http://apbs.sourceforge.net/ or at http://www.nbcr.net. This APBS Roll contains the latest APBS version 1.2.1b and PDB2PQR package version 1.5. The APBS Roll can be downloaded from the APBS download site http://sourceforge.net/projects/apbs and the Roll documentation including installation and usage information is available at http://nbcr.net/software/doc/apbs-roll/5.3/ Questions or comments about the roll may be directed to Robert Konecny <ro...@uc...>. |
From: Nathan B. <ba...@bi...> - 2009-12-03 02:26:40
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Dear APBS Users -- APBS 1.2.1 has been released. This is a bugfix release specifically aimed at addressing a problem with certain nonlinear Poisson-Boltzmann calculations. In particular, several users noticed that Poisson-Boltzmann calculations which focused into a low dielectric region would occasionally generate very large (~1E25 kJ/mol) energies. This was due to a bug that caused instability in the nonlinear Poisson-Boltzmann solver. This bug has been fixed in this release. The full list of changes is: • Added in warning into focusFillBound if there is a large value detected in setting the boundary conditions during a focusing calculation • Added in a check and abort in Vpmg_qmEnergy if chopped values are detected. This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions. • Fixed a bug in Vpmg_MolIon that causes npbe based calculations to return very large energies. This occurs under certain conditions for NPBE calculations where focusing cuts into a low-dielectric regions. More information about APBS as well as download links can be obtained from http://www.poissonboltzmann.org/. We apologize for this bug and thank you for your continued support of APBS. Sincerely, The APBS Development Team — Nathan Baker (http://bakergroup.wustl.edu/) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis |